FMO DATABASE

FMODB ID: 3Z2RL

Calculation Name: 1E87-A-Xray547

Preferred Name: Early activation antigen CD69

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 1E87

Chain ID: A

ChEMBL ID: CHEMBL3308911

UniProt ID: Q07108

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1058562.645027
FMO2-HF: Nuclear repulsion	1009316.103833
FMO2-HF: Total energy	-49246.541193
FMO2-MP2: Total energy	-49386.262225

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:83:SER)

Summations of interaction energy for fragment #1(A:83:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-31.597	-28.599	4.425	-3.735	-3.687	-0.041

Interaction energy analysis for fragmet #1(A:83:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.915

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	85	CYS	0	-0.004	0.036	2.945	13.335	15.029	0.024	-0.692	-1.026	0.000
4	A	86	SER	0	0.041	0.011	2.049	-39.140	-38.145	4.401	-2.980	-2.416	-0.041
5	A	87	GLU	-1	-0.924	-0.965	4.064	-56.913	-56.604	0.000	-0.063	-0.245	0.000
6	A	88	ASP	-1	-0.915	-0.945	5.795	-26.950	-26.950	0.000	0.000	0.000	0.000
7	A	89	TRP	0	-0.070	-0.043	7.015	3.376	3.376	0.000	0.000	0.000	0.000
8	A	90	VAL	0	0.001	0.010	7.519	-3.054	-3.054	0.000	0.000	0.000	0.000
9	A	91	GLY	0	0.056	0.010	7.617	0.968	0.968	0.000	0.000	0.000	0.000
10	A	92	TYR	0	-0.043	-0.029	8.542	1.546	1.546	0.000	0.000	0.000	0.000
11	A	93	GLN	0	0.018	-0.003	11.943	0.250	0.250	0.000	0.000	0.000	0.000
12	A	94	ARG	1	0.907	0.953	9.656	26.989	26.989	0.000	0.000	0.000	0.000
13	A	95	LYS	1	0.843	0.936	11.995	17.865	17.865	0.000	0.000	0.000	0.000
14	A	97	TYR	0	-0.018	-0.023	9.828	2.999	2.999	0.000	0.000	0.000	0.000
15	A	98	PHE	0	0.053	0.029	11.296	-1.793	-1.793	0.000	0.000	0.000	0.000
16	A	99	ILE	0	-0.006	0.006	13.556	1.185	1.185	0.000	0.000	0.000	0.000
17	A	100	SER	0	-0.012	0.004	17.019	-0.291	-0.291	0.000	0.000	0.000	0.000
18	A	101	THR	0	0.057	0.019	19.051	0.344	0.344	0.000	0.000	0.000	0.000
19	A	102	VAL	0	-0.004	-0.002	21.589	0.706	0.706	0.000	0.000	0.000	0.000
20	A	103	LYS	1	0.877	0.947	24.074	10.539	10.539	0.000	0.000	0.000	0.000
21	A	104	ARG	1	0.872	0.932	23.671	13.276	13.276	0.000	0.000	0.000	0.000
22	A	105	SER	0	0.082	0.060	27.311	-0.224	-0.224	0.000	0.000	0.000	0.000
23	A	106	TRP	0	0.031	0.008	25.608	-0.354	-0.354	0.000	0.000	0.000	0.000
24	A	107	THR	0	0.032	-0.005	25.944	-0.503	-0.503	0.000	0.000	0.000	0.000
25	A	108	SER	0	0.028	0.020	26.220	-0.491	-0.491	0.000	0.000	0.000	0.000
26	A	109	ALA	0	-0.016	0.002	23.021	-0.460	-0.460	0.000	0.000	0.000	0.000
27	A	110	GLN	0	0.062	0.023	21.547	-1.028	-1.028	0.000	0.000	0.000	0.000
28	A	111	ASN	0	-0.007	-0.012	21.436	-0.668	-0.668	0.000	0.000	0.000	0.000
29	A	112	ALA	0	0.033	0.016	20.201	-0.420	-0.420	0.000	0.000	0.000	0.000
30	A	113	CYS	0	-0.113	-0.015	15.160	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	114	SER	0	0.022	0.013	16.705	-1.250	-1.250	0.000	0.000	0.000	0.000
32	A	115	GLU	-1	-0.930	-0.957	17.787	-15.355	-15.355	0.000	0.000	0.000	0.000
33	A	116	HIS	0	-0.034	-0.004	12.786	-1.955	-1.955	0.000	0.000	0.000	0.000
34	A	117	GLY	0	-0.001	0.005	12.720	-2.219	-2.219	0.000	0.000	0.000	0.000
35	A	118	ALA	0	-0.108	-0.050	13.426	-1.095	-1.095	0.000	0.000	0.000	0.000
36	A	119	THR	0	0.005	-0.008	15.280	1.493	1.493	0.000	0.000	0.000	0.000
37	A	120	LEU	0	0.014	0.001	17.677	-0.880	-0.880	0.000	0.000	0.000	0.000
38	A	121	ALA	0	-0.013	0.000	18.105	0.245	0.245	0.000	0.000	0.000	0.000
39	A	122	VAL	0	-0.006	-0.003	18.734	0.968	0.968	0.000	0.000	0.000	0.000
40	A	123	ILE	0	-0.004	0.000	19.250	-0.887	-0.887	0.000	0.000	0.000	0.000
41	A	124	ASP	-1	-0.815	-0.898	20.044	-14.746	-14.746	0.000	0.000	0.000	0.000
42	A	125	SER	0	-0.017	-0.009	20.086	0.351	0.351	0.000	0.000	0.000	0.000
43	A	126	GLU	-1	-0.742	-0.878	22.495	-12.325	-12.325	0.000	0.000	0.000	0.000
44	A	127	LYS	1	0.898	0.959	18.540	15.799	15.799	0.000	0.000	0.000	0.000
45	A	128	ASP	-1	-0.788	-0.900	17.358	-18.158	-18.158	0.000	0.000	0.000	0.000
46	A	129	MET	0	0.024	0.027	19.280	-0.345	-0.345	0.000	0.000	0.000	0.000
47	A	130	ASN	0	-0.046	-0.045	22.535	0.270	0.270	0.000	0.000	0.000	0.000
48	A	131	PHE	0	-0.088	-0.031	14.012	0.056	0.056	0.000	0.000	0.000	0.000
49	A	132	LEU	0	0.048	0.013	18.044	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	133	LYS	1	0.949	0.986	20.034	11.871	11.871	0.000	0.000	0.000	0.000
51	A	134	ARG	1	0.914	0.954	19.054	15.745	15.745	0.000	0.000	0.000	0.000
52	A	135	TYR	0	-0.040	-0.019	13.842	-0.092	-0.092	0.000	0.000	0.000	0.000
53	A	136	ALA	0	0.050	0.034	19.138	-0.062	-0.062	0.000	0.000	0.000	0.000
54	A	137	GLY	0	-0.027	-0.004	22.000	0.304	0.304	0.000	0.000	0.000	0.000
55	A	138	ARG	1	0.946	0.950	24.234	12.706	12.706	0.000	0.000	0.000	0.000
56	A	139	GLU	-1	-0.847	-0.917	26.358	-10.393	-10.393	0.000	0.000	0.000	0.000
57	A	140	GLU	-1	-0.858	-0.902	26.492	-10.735	-10.735	0.000	0.000	0.000	0.000
58	A	141	HIS	0	-0.040	-0.038	21.431	-0.576	-0.576	0.000	0.000	0.000	0.000
59	A	142	TRP	0	-0.044	-0.033	24.328	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	143	VAL	0	0.014	-0.004	21.480	-0.845	-0.845	0.000	0.000	0.000	0.000
61	A	144	GLY	0	-0.011	0.002	22.322	0.500	0.500	0.000	0.000	0.000	0.000
62	A	145	LEU	0	-0.030	-0.008	23.208	0.135	0.135	0.000	0.000	0.000	0.000
63	A	146	LYS	1	0.882	0.913	26.872	10.277	10.277	0.000	0.000	0.000	0.000
64	A	147	LYS	1	0.924	0.969	29.863	8.780	8.780	0.000	0.000	0.000	0.000
65	A	148	GLU	-1	-0.791	-0.874	32.582	-9.602	-9.602	0.000	0.000	0.000	0.000
66	A	149	PRO	0	0.027	-0.006	35.804	0.102	0.102	0.000	0.000	0.000	0.000
67	A	150	GLY	0	0.006	0.013	39.610	0.006	0.006	0.000	0.000	0.000	0.000
68	A	151	HIS	0	-0.057	-0.019	35.954	0.005	0.005	0.000	0.000	0.000	0.000
69	A	152	PRO	0	-0.006	-0.010	34.543	0.019	0.019	0.000	0.000	0.000	0.000
70	A	153	TRP	0	-0.013	-0.010	31.055	-0.140	-0.140	0.000	0.000	0.000	0.000
71	A	154	LYS	1	0.942	0.966	28.282	10.201	10.201	0.000	0.000	0.000	0.000
72	A	155	TRP	0	0.042	0.017	23.665	-0.307	-0.307	0.000	0.000	0.000	0.000
73	A	156	SER	0	-0.040	-0.017	21.394	0.215	0.215	0.000	0.000	0.000	0.000
74	A	157	ASN	0	-0.005	-0.008	19.875	0.577	0.577	0.000	0.000	0.000	0.000
75	A	158	GLY	0	0.006	0.007	22.752	0.050	0.050	0.000	0.000	0.000	0.000
76	A	159	LYS	1	0.852	0.938	21.976	14.445	14.445	0.000	0.000	0.000	0.000
77	A	160	GLU	-1	-0.898	-0.950	26.309	-10.051	-10.051	0.000	0.000	0.000	0.000
78	A	161	PHE	0	-0.015	-0.013	27.530	-0.437	-0.437	0.000	0.000	0.000	0.000
79	A	162	ASN	0	0.031	0.003	27.530	0.291	0.291	0.000	0.000	0.000	0.000
80	A	163	ASN	0	-0.039	-0.024	30.762	0.278	0.278	0.000	0.000	0.000	0.000
81	A	164	TRP	0	-0.049	-0.018	24.442	0.288	0.288	0.000	0.000	0.000	0.000
82	A	165	PHE	0	0.007	0.004	26.072	0.043	0.043	0.000	0.000	0.000	0.000
83	A	166	ASN	0	0.030	0.001	30.803	0.114	0.114	0.000	0.000	0.000	0.000
84	A	167	VAL	0	-0.017	0.002	30.874	-0.230	-0.230	0.000	0.000	0.000	0.000
85	A	168	THR	0	0.017	0.021	33.387	0.335	0.335	0.000	0.000	0.000	0.000
86	A	169	GLY	0	0.066	0.047	35.295	-0.193	-0.193	0.000	0.000	0.000	0.000
87	A	170	SER	0	0.007	-0.001	37.839	0.107	0.107	0.000	0.000	0.000	0.000
88	A	171	ASP	-1	-0.836	-0.904	35.563	-8.420	-8.420	0.000	0.000	0.000	0.000
89	A	172	LYS	1	0.872	0.907	34.490	8.290	8.290	0.000	0.000	0.000	0.000
90	A	173	CYS	0	-0.081	-0.027	29.437	-0.424	-0.424	0.000	0.000	0.000	0.000
91	A	174	VAL	0	0.033	0.020	27.776	0.260	0.260	0.000	0.000	0.000	0.000
92	A	175	PHE	0	-0.037	-0.012	26.753	-0.582	-0.582	0.000	0.000	0.000	0.000
93	A	176	LEU	0	-0.004	-0.011	22.563	0.194	0.194	0.000	0.000	0.000	0.000
94	A	177	LYS	1	0.849	0.934	25.577	9.926	9.926	0.000	0.000	0.000	0.000
95	A	178	ASN	0	0.005	-0.011	26.212	0.221	0.221	0.000	0.000	0.000	0.000
96	A	179	THR	0	-0.011	-0.012	27.066	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	180	GLU	-1	-0.934	-0.968	29.462	-9.401	-9.401	0.000	0.000	0.000	0.000
98	A	181	VAL	0	0.003	-0.016	27.163	-0.511	-0.511	0.000	0.000	0.000	0.000
99	A	182	SER	0	-0.010	-0.005	29.724	0.437	0.437	0.000	0.000	0.000	0.000
100	A	183	SER	0	-0.026	-0.021	30.959	-0.279	-0.279	0.000	0.000	0.000	0.000
101	A	184	MET	0	-0.020	-0.010	31.965	0.137	0.137	0.000	0.000	0.000	0.000
102	A	185	GLU	-1	-0.875	-0.945	33.345	-8.574	-8.574	0.000	0.000	0.000	0.000
103	A	187	GLU	-1	-0.866	-0.934	31.376	-9.428	-9.428	0.000	0.000	0.000	0.000
104	A	188	LYS	1	0.904	0.970	31.803	9.416	9.416	0.000	0.000	0.000	0.000
105	A	189	ASN	0	0.010	-0.019	29.738	-0.306	-0.306	0.000	0.000	0.000	0.000
106	A	190	LEU	0	-0.007	0.003	27.366	0.281	0.281	0.000	0.000	0.000	0.000
107	A	191	TYR	0	0.005	0.015	23.056	0.069	0.069	0.000	0.000	0.000	0.000
108	A	192	TRP	0	0.021	-0.009	19.101	0.634	0.634	0.000	0.000	0.000	0.000
109	A	193	ILE	0	0.028	0.012	16.812	-0.664	-0.664	0.000	0.000	0.000	0.000
110	A	195	ASN	0	-0.051	-0.041	13.707	-0.553	-0.553	0.000	0.000	0.000	0.000
111	A	196	LYS	1	0.961	0.986	9.114	30.115	30.115	0.000	0.000	0.000	0.000
112	A	197	PRO	0	0.006	-0.007	12.041	-1.017	-1.017	0.000	0.000	0.000	0.000
113	A	198	TYR	0	-0.064	-0.041	7.674	-1.490	-1.490	0.000	0.000	0.000	0.000
114	A	199	LYS	0	0.041	0.040	6.329	-4.665	-4.665	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:83:SER)